Obi-Wan and Anakin infiltrate Count Dooku's frigate in an attempt to capture him but all three end up crash-landing on the planet Vanqor instead. While the Jedi are busy fighting a mother Gundark, Dooku falls into the hands of a pirate gang led Hondo Ohnaka. The pirate chief then offers Dooku up for ransom to the Republic in exchange for a million credits worth of spice.
Obi-Wan and Anakin are now hostages along with Dooku at Hondo Ohnaka's stronghold on Florrum. Delegate Jar Jar Binks and Senator Kharrus arrive with the ransom and a battalion of troopers, only to find there is treason within the pirate ranks.
General Skywalker is injured while rescuing fellow Jedi General Aayla Secura from Super Battle Droids equipped with rocket packs. Ahsoka Tano crash-lands their shuttle on the neutral planet of Maridun, where the native Lurmen villagers refuse to takes sides in the war. They are however willing to send a healer to help Anakin.
A separatist fleet led by Neimodian Lok Durd arrives on Maridun to test their new defoliator weapon, which destroys organic live but leaves machines intact. Unknown to them, three Jedi and two Clone Troopers are stuck nearby without a means of transport off planet. When the Lurmen village becomes endangered by the test, the Jedi rush to defend it, despite the objections of village elder Tee Watt Kaa.
Obi-Wan, Anakin and a detachment of the 501st investigate the slaughter of a Republic outpost on Orto Plutonia. They soon find a Separatist base destroyed by the same aggressors, who turn out to be a clan of native Talz that just want to be left alone. Unfortunately Pantoran dignitary Chi Cho claims the planet to be under his people's jurisdiction and orders the unwanted aliens to be either removed or wiped out. As the Jedi cannot interfere, the only hope for a peaceful resolution lies with young senator Riyo Chuchi.
Evil scientist Dr. Nuvo Vindi is recreating the dreaded Blue Shadow Virus in his secret underground lab on Naboo. When he captures Senator Amidala and Representative Binks, Jedi Generals Skywalker & Kenobi mount a rescue operation.
The deadly Blue Shadow Virus is unleashed in Vindi's underground lab with Padmé, Ahsoka, Jar Jar and several Clone troopers stuck in it. Anakin and Obi-Wan have just 48 hours to find a cure. They travel to the moons of Iego but will have a hard time trying to get past the 'Ghost of Drol' in order to leave again.
During the battle for Ryloth, Obi-Wan, Commander Cody and his 212th Attack Battalion set out to free the occupied Twi'lek village of Nabat. Two troopers, Waxer and Boil find a young girl named Numa who becomes instrumental in Obi-Wan's plan.
Cad Bane has gathered a team of his fellow bounty hunters to seize control of the Senate Building. The plan is to exchange the hostages therein for the freedom of crime lord Ziro the Hutt. Anakin Skywalker is the sole Jedi left in the building, but unfortunately he has left his light saber in Senator Amidala's possession.
The Jedi council suspects Senator Rush Clovis of the Banking Delegation is working with the Trade Federation. They ask his former lover Senator Amidala to get reacquainted with him and act as a spy. When she accompanies Clovis on a trip to Cato Neimodia, Anakin Skywalker goes along disguised as a Naboo pilot.
Jedi Generals Ki-Adi-Mundi, Obi-Wan Kenobi and Anakin Skywalker return to Geonosis, the very battleground where the Clone Wars first erupted. Their mission is to destroy Poggle the Lessers ray shielded droid factories in an attempt to give the outnumbered Clone army a fighting chance.
Poggle the Lesser is about to unleash his brand new super-tanks. Anakin Skywalker and Luminara Unduli provide a frontal assault on Poggles factory while their Padawans Ahsoka Tano and Barris Offee sneak in through the underground catacombs.
Ahsoka, Barris and Tango Company board a supply ship to a station near Ord Cestus. But one of the troopers has been infected by a Geonosian brain worm and has taken along a nest full of worm eggs to submit the others.